Fungi 2011 project - Differential expression analysis for KEGG ortholog network
Alonso Serrano
2020-04-07
1 Introduction
This file contains the script and results for the differential expression analysis done to the fungi 2011 data, based on the KEGG orthologs.
- 20191220 Updated with 2019-12-20 files from John
- 20200407 Added treatment DE in new section
1.1 Prerequisites
KEGG ortholog file
A metadata file containing all the information related to each sample, file name, time, condition and replica number.
2 Setup
Load libraries
library(DESeq2)
library(tximport)
library(BiocParallel)
library(plotly)
library(dplyr)
library(here)
register(MulticoreParam(4))
source(here("Rtoolbox/src/utilsDE.r"))
source(here("/Rtoolbox/src/plot3Dvector.R"))
source(here("/Rtoolbox/src/plotVectorPCA.R"))
source(here("Rtoolbox/src/plotEnrichedTreemap.R"))
source(here("Rtoolbox/src/plotUpAndDown.R"))
source(here("UPSCb-common/src/R/gopher.R"))plotResults <- function(theData) {
for (deName in names(theData)) {
#deName <- paste0('Cluster',clus)
#clusIndex <- match(deName, names(theClusters))
#clusIndex <- as.numeric(substr(deName,8,nchar(deName)))
cat(paste0("<H3>", deName, "","</H3>"))
cat("\n\n")
enrUp <- theData[[deName]]$up[['ko_pathway']]
enrDown <- theData[[deName]]$down[['ko_pathway']]
cat("Up genes \n\n")
if (!is.null(enrUp) ) {
plotEnrichedTreemap(theData[[deName]]$up, enrichment = 'ko_pathway', namespace = 'none',
de='up', title = paste(deName," KO enrichment"))
} else {
cat("No enrichment data found")
}
cat("\n")
cat("<hr>")
cat("Down genes \n\n")
if (!is.null(enrDown) ) {
plotEnrichedTreemap(theData[[deName]]$down, enrichment = 'ko_pathway', namespace = 'none',
de='down', title = paste(deName," KO enrichment"))
} else {
cat("No enrichment data found")
}
cat("\n")
cat("<hr>")
}
}
getDEenrichment <- function(deData, background){
results <- lapply(deData, function(x){
upGenes <- rownames(x[x$log2FoldChange>0,])
downGenes <- rownames(x[x$log2FoldChange<0,])
upEnr <- list(ko_pathway=NULL)
downEnr <- list(ko_pathway=NULL)
if(length(upGenes)>1)
upEnr <- gopher(upGenes, task=list("ko_pathway"), background=background, url='ko', alpha=0.05)
if(length(downGenes)>1)
downEnr <- gopher(downGenes, task=list("ko_pathway"), background=background, url='ko', alpha=0.05)
res <- list(up=upEnr, down=downEnr)
res
})
results
}Set the project folder
projectFolder <- "/mnt/picea/projects/spruce/vhurry/fungi-flakaliden-2011"
deFolder <- file.path(projectFolder,"DE")
dataFolder <- file.path(projectFolder,"data")Read metadata
meta <- read.table(file.path(dataFolder, "meta.tsv"), header = TRUE, sep = '\t', comment.char = "", stringsAsFactors = TRUE)
meta$Treatment <- ifelse(meta$Condition == 'control', 'C', 'F')
meta$Week <- meta$Sampling.date..week..
meta$group <- paste0(meta$Week, gsub("T","F",meta$Plot))
meta <- meta[order(meta$group), ]
meta$group <- substr(meta$group, 1, 4)
meta$group <- as.factor(meta$group)
meta$Treatment <- as.factor(meta$Treatment)
data <- read.table(file.path(dataFolder, "kingdom.Fungi.kos.raw.tsv"), header = T, sep='\t', comment.char = "", quote="", row.names = 1)
rownames(data) <- substr(rownames(data), 1, 6)
colnames(data)<-gsub("X", "", colnames(data))
#' #remove non usefull samples
data <- data[,colnames(data) %in% meta$Sample.ID]
#' #Order them by group
data <- data[, match(meta$Sample.ID, colnames(data))]
#' change the names of the samples to group
colnames(data) <- paste0(meta$Sampling.date..week..,meta$Plot)Add the interaction group to the metadata, in order to simplify
head(meta, n=3)## Sample.ID Plot Condition Sampling.date..week..
## 1 229_1 C1 control W19
## 12 229_2 C2 control W19
## 23 229_3 C3 control W19
## Raw.data.location
## 1 swestore/N.Street_12_01/120626_BC0YAHACXX
## 12 swestore/N.Street_12_01/120626_BC0YAHACXX
## 23 swestore/N.Street_12_01/120626_BC0YAHACXX
## Sequence.File.Name Treatment Week group
## 1 1_120626_BC0YAHACXX_229_1_index1_1.fastq.gz C W19 W19C
## 12 2_120626_BC0YAHACXX_229_2_index1_1.fastq.gz C W19 W19C
## 23 3_120626_BC0YAHACXX_229_3_index1_1.fastq.gz C W19 W19CImport data as a DESeq object and place the sample names to the columns
ddsMatrix <- DESeqDataSetFromMatrix(data, colData=meta, design = ~group)1 KO have 0 expression accross all samples we can remove it
ddsMatrix <- ddsMatrix[(rowSums(counts(ddsMatrix)) > 0),]We save the gene names of all expressed genes for future uses
write.table(rownames(assay(ddsMatrix)), file=file.path(deFolder, "background.txt"), sep='\t', row.names = F, col.names=F, quote = F)3 QA
3.1 PCA
We use blind vst to plot a PCA and check for patterns and outliers
vsd.QA <- vst(ddsMatrix, blind=TRUE)geneNumber <- length(rownames(assay(vsd.QA))) #4259
plotPCA(vsd.QA, intgroup = c("Treatment", "Week"), ntop=geneNumber)
The PCA shows a possbile outlier in T:W32 To get which replicate is the outlier we use the pairs function
pairs(~W32F1+W32F2+W32F3,
data=data.frame(t(t(assay(vsd.QA))[c('W32F1','W32F2', 'W32F3'),])),
lower.panel = panel.smooth,
upper.panel = panel.cor,
main="Replicate scatterplot",
gap=0, row1attop=FALSE)
There is not enought evidence to say it is an outlier, we keep the replicate.
The PCA seems correct. We plot the same PCAs but using different colors to focus on the time or the treatment
3.2 PCA for treatment group
plotPCA(vsd.QA, intgroup = c("Treatment"), ntop=geneNumber) 
3.3 PCA for time group
plotPCA(vsd.QA, intgroup = c("Week"), ntop=geneNumber) 
3.4 Focused PCA
We plot a PCA with letters instead of numbers for increased clarity
vsd.QA.t <- t(assay(vsd.QA))
pca <- prcomp(vsd.QA.t)
percents <- round(summary(pca)$importance[2,]*100)
pchs <- LETTERS[as.integer(factor(substr(rownames(vsd.QA.t), 2, 3)))]
cols <- c("#fc8d62", "#66c2a5")[as.integer(factor(substr(rownames(vsd.QA.t),4,4)))]
PCAlegend <- data.frame(pchs, substr(rownames(vsd.QA.t), 2, 3))
par(oma = c(4, 1, 1, 4))
plot(pca$x[,1], pca$x[,2],
xlab=paste("Comp. 1 (",percents[1],"%)",sep=""),
ylab=paste("Comp. 2 (",percents[2],"%)",sep=""),
col=cols,pch=pchs, cex = 1.0, main="")
par(fig = c(0, 1, 0, 1), oma = c(0, 0, 0, 0), mar = c(0, 0, 0, 0), new = TRUE)
plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
legend("topright", legend=unique(PCAlegend$pchs:meta$Week), cex = 0.8, xpd=TRUE)
legend("bottomright", legend=unique(meta$Treatment), fill=unique(cols),cex = 0.8, xpd=TRUE)
3.5 Vector plot
We can better observe the tendencies by drawing a vector from the mean of the control samples (within one week) to the mean of the fertilised samples
plotVectorPCA(vsd.QA.t, meta, c("Treatment", "Week"))## PC1 PC2 binaryCondition secondaryCondition
## W19C1 -12.835564 -3.12885644 C W19
## W19C2 -7.136930 -0.35194390 C W19
## W19C3 14.183493 2.39117143 C W19
## W19F1 16.245043 6.26750650 F W19
## W19F2 15.561554 -0.84498498 F W19
## W19F3 15.773964 2.01257830 F W19
## W20C1 -7.240336 13.32511629 C W20
## W20C2 7.541405 15.16444695 C W20
## W20C3 -8.630629 14.17918425 C W20
## W20F1 16.451628 -3.53455768 F W20
## W20F2 10.026946 11.34902397 F W20
## W20F3 15.829096 4.54957761 F W20
## W21C1 -8.949417 5.80983419 C W21
## W21C2 -12.867080 5.69695114 C W21
## W21C3 -13.469569 3.34434660 C W21
## W21F1 9.693915 9.83281110 F W21
## W21F2 10.629653 5.05514759 F W21
## W21F3 12.472369 1.84122680 F W21
## W22C1 2.465428 -3.26535011 C W22
## W22C2 -1.862445 -5.46583851 C W22
## W22C3 -19.835964 -9.96697938 C W22
## W22F1 20.381534 -4.40381276 F W22
## W22F2 17.687297 -0.76851080 F W22
## W22F3 15.545575 -11.44788945 F W22
## W23C1 -20.832584 -2.19062063 C W23
## W23C2 -25.746630 -5.85008782 C W23
## W23C3 -20.322730 -5.64346017 C W23
## W23F1 15.173941 -3.15605688 F W23
## W23F2 18.320859 -2.33551262 F W23
## W23F3 18.380947 -1.66034616 F W23
## W24C1 -5.836818 2.31484431 C W24
## W24C2 -4.838320 1.71167723 C W24
## W24C4 -10.078574 4.37746295 C W24
## W24F1 16.204199 -3.72194060 F W24
## W24F2 18.133096 1.56881222 F W24
## W24F3 19.510890 -12.90505297 F W24
## W25C1 -13.226848 -1.45201780 C W25
## W25C2 -8.351215 -2.69203984 C W25
## W25C3 2.031165 17.49065103 C W25
## W25F1 21.807421 -19.41806921 F W25
## W25F2 22.355072 -6.72235892 F W25
## W25F3 26.601569 6.13374644 F W25
## W26C1 -30.162602 -19.58651328 C W26
## W26C2 -30.269755 -18.23145481 C W26
## W26C3 -20.511743 -8.04298772 C W26
## W26F2 19.749310 -10.91829386 F W26
## W26F3 18.332146 -14.92259525 F W26
## W26F4 21.201130 -11.20785259 F W26
## W28C3 -15.735152 5.66627242 C W28
## W28C4 -24.747088 -8.24755058 C W28
## W28F1 19.822460 -0.93126127 F W28
## W28F3 18.980834 9.11385187 F W28
## W28F4 17.636153 8.24813634 F W28
## W31C1 -17.770261 -5.79448245 C W31
## W31C2 -24.368006 -14.33852950 C W31
## W31C3 -13.501973 -0.06215974 C W31
## W31F1 17.122696 -17.70396387 F W31
## W31F2 20.184216 0.24581197 F W31
## W31F3 20.879665 10.10539310 F W31
## W32C1 -10.828655 1.43569513 C W32
## W32C2 -11.839453 4.62643158 C W32
## W32C4 -16.304342 2.15705298 C W32
## W32F1 19.177610 -36.65346241 F W32
## W32F2 8.069678 4.88385351 F W32
## W32F3 17.909912 -11.69903249 F W32
## W34C2 -21.603676 -3.10491857 C W34
## W34C3 -14.569326 5.26198852 C W34
## W34F2 2.430427 4.68228090 F W34
## W34F3 2.451473 4.92107840 F W34
## W34F4 4.124377 6.07246988 F W34
## W35C1 -17.693121 -1.63178483 C W35
## W35C2 -19.655108 -7.39498160 C W35
## W35C4m -24.904877 -10.73745267 C W35
## W35F2 11.554248 12.72621801 F W35
## W35F3 23.074395 10.48754208 F W35
## W35F4m 6.990583 11.46821952 F W35
## W36C2 -22.141842 -1.24085376 C W36
## W36C3 -22.284629 -1.30224094 C W36
## W36C4 -17.266884 -3.58293586 C W36
## W36F1 7.625603 -3.91462615 F W36
## W36F3 -3.977360 0.58653926 F W36
## W36F4 -2.661694 4.57600353 F W36
## W37C1 -16.487110 3.06087762 C W37
## W37C2 -16.307199 1.27383904 C W37
## W37C3 -13.077152 5.29698511 C W37
## W37F1 15.637748 -2.61136179 F W37
## W37F2 12.580327 -9.19056558 F W37
## W37F3 -14.720666 8.26278746 F W37
## W38C1 -15.373497 7.21528917 C W38
## W38C2 -13.833696 7.77866643 C W38
## W38C3 -23.232426 -2.79269242 C W38
## W38F2 4.902759 -0.43840661 F W38
## W38F3 11.096051 -4.13355488 F W38
## W38F4 8.166305 1.60897116 F W38
## W39C1 -18.411294 6.07710463 C W39
## W39C2 -9.116810 13.26627977 C W39
## W39C3 -14.734182 8.34707427 C W39
## W39F1 20.718512 -7.57592452 F W39
## W39F2 18.348266 -1.20823749 F W39
## W39F3 13.355431 13.89873801 F W39
## W40C2 -9.035417 9.38062865 C W40
## W40C3 -9.475316 8.03444473 C W40
## W40C4 -27.736738 -12.09662446 C W40
## W40F1 17.917298 6.48729706 F W40
## W40F2 -9.451951 7.03095384 F W40
## W40F3 -9.961948 8.12195307 F W40
## W41C1 -9.527212 7.51306211 C W41
## W41C2 -9.709003 8.08361965 C W41
## W41C3 18.363678 10.61573701 C W41
## W41F1 13.622298 -14.22261043 F W41
## W41F2 14.017174 -6.58906468 F W41
Also, we can plot it in 3D to include PC3
plot3DVectorPCA(pca, meta$Week, meta$Treatment)3.6 Scree plot
We can see how PC proportions are distributed
screePlot(pca, 10)
The first 5 components explain 62 % of the variance
summary(pca)$importance[2,][1:5] *100## PC1 PC2 PC3 PC4 PC5
## 36.577 10.895 6.771 4.681 3.360sum(summary(pca)$importance[2,][1:5]) * 100## [1] 62.2843.7 PCA bi-plot comparition
As seen before, we can focus on the 5 components and plot a comparative bi-plot
par(cex=1.0, cex.axis=0.8, cex.main=0.8)
pairs(pca$x[,1:5], col=cols, main="Principal components analysis bi-plot\nPCs 1-5", pch=pchs)
3.8 3D PCA
We represent the first 3 compoments as a 3D interactive object
colors <- c("#F8766D", "#00BFC4", "#56B4E9")
treatment <- substr(rownames(vsd.QA.t), 4, 4)
treatment[treatment == 'C'] <- 'Control'
treatment[treatment == 'F'] <- 'Fertilised'
df3D <- data.frame(treatment)
df3D$time <- substr(rownames(vsd.QA.t),2,3)
df3D$colors <- colors[as.numeric(df3D$treatment)]
df3D$PC1 <- pca$x[,1]
df3D$PC2 <- pca$x[,2]
df3D$PC3 <- pca$x[,3]
plot_ly(df3D, x = ~PC1, y = ~PC3, z = ~PC2,
color = ~treatment, colors = c("#F8766D", "#00BFC4"),
text = ~paste("Week:", time, '<br>Treatment:', treatment) ) %>%
add_markers() %>%
layout(scene = list(xaxis = list(title = paste("PC1 (",percents[1],"%)",sep="")),
yaxis = list(title = paste("PC3 (",percents[3],"%)",sep="")),
zaxis = list(title = paste("PC2 (",percents[2],"%)",sep=""))))4 Differential Expression
The dataset is ready for DESeq2. We check the design of the DE object
design(ddsMatrix)## ~groupWe are interested on future comparitions like DE ko in each timepoints or between timepoints that is why we created the interaction group
4.1 Run DESeq
dds <- DESeq(ddsMatrix)We check the result names
resultsNames(dds)## [1] "Intercept" "group_W19F_vs_W19C" "group_W20C_vs_W19C"
## [4] "group_W20F_vs_W19C" "group_W21C_vs_W19C" "group_W21F_vs_W19C"
## [7] "group_W22C_vs_W19C" "group_W22F_vs_W19C" "group_W23C_vs_W19C"
## [10] "group_W23F_vs_W19C" "group_W24C_vs_W19C" "group_W24F_vs_W19C"
## [13] "group_W25C_vs_W19C" "group_W25F_vs_W19C" "group_W26C_vs_W19C"
## [16] "group_W26F_vs_W19C" "group_W28C_vs_W19C" "group_W28F_vs_W19C"
## [19] "group_W31C_vs_W19C" "group_W31F_vs_W19C" "group_W32C_vs_W19C"
## [22] "group_W32F_vs_W19C" "group_W34C_vs_W19C" "group_W34F_vs_W19C"
## [25] "group_W35C_vs_W19C" "group_W35F_vs_W19C" "group_W36C_vs_W19C"
## [28] "group_W36F_vs_W19C" "group_W37C_vs_W19C" "group_W37F_vs_W19C"
## [31] "group_W38C_vs_W19C" "group_W38F_vs_W19C" "group_W39C_vs_W19C"
## [34] "group_W39F_vs_W19C" "group_W40C_vs_W19C" "group_W40F_vs_W19C"
## [37] "group_W41C_vs_W19C" "group_W41F_vs_W19C"In order to make all the comparitions automated, we prepare vectors with the elements that will be used in the result extraction
controlVector <- as.character(unique(meta$group[grep("C", meta$group)]))
fertilisedVector <- as.character(unique(meta$group[grep("F", meta$group)]))4.2 Result extraction
We want to make 3 different comparations, each one composed of several outputs from DESeq2 In order to do that, we will extract all the results for each comparation type, store them as a list and then we can process them.
4.2.1 Control week vs week
For this comparition we take consider only the control condition and we compare each pair of weeks to determine which genes are up or down regaluated from one week to the previous week
control.res <- mapply(getRes, controlVector[-1],
controlVector[-length(controlVector)],
MoreArgs = list(localDDS=dds, group="group"))4.2.2 Fertilised week vs week
For this comparition we take consider only the fertilised condition and we compare each pair of weeks to determine which genes are up or down regaluated from one week to the previous week
fertilised.res <- mapply(getRes, fertilisedVector[-1],
fertilisedVector[-length(fertilisedVector)],
MoreArgs = list(localDDS=dds, group="group"))4.2.3 Timepoint Fertilised vs Control
For this comparition we take consider only a week each time and then compare DE genes due to fertilisation
combined.res <- mapply(getRes, fertilisedVector, controlVector,
MoreArgs = list(localDDS=dds, group="group"))We add the corresponding names to the results
names(control.res) <- c("20Cvs19C", "21Cvs20C", "22Cvs21C", "23Cvs22C",
"24Cvs23C", "25Cvs24C", "26Cvs25C", "28Cvs26C",
"31Cvs28C", "32Cvs31C", "34Cvs32C", "35Cvs34C",
"36Cvs35C", "37Cvs36C", "38Cvs37C", "39Cvs38C",
"40Cvs39C", "41Cvs40C")
names(fertilised.res) <- c("20Fvs19F", "21Fvs20F", "22Fvs21F", "23Fvs22F",
"24Fvs23F", "25Fvs24F", "26Fvs25F", "28Fvs26F",
"31Fvs28F", "32Fvs31F", "34Fvs32F", "35Fvs34F",
"36Fvs35F", "37Fvs36F", "38Fvs37F", "39Fvs38F",
"40Fvs39F", "41Fvs40F")
names(combined.res) <- c("19Fvs19C", "20Fvs20C", "21Fvs21C", "22Fvs22C",
"23Fvs23C", "24Fvs24C", "25Fvs25C", "26Fvs26C",
"28Fvs28C", "31Fvs31C", "32Fvs32C", "34Fvs34C",
"35Fvs35C", "36Fvs36C", "37Fvs37C", "38Fvs38C",
"39Fvs39C", "40Fvs40C", "41Fvs41C")4.3 Filtering
The results contain all the genes, we need to filter them to get only those genes that are stadistical significant and that have a strong condtition effect For that we discard all the genes that has a padj higher than 0.01 and a log2FoldChange lower than 0.5 (absolute value)
control.res.filter <- lapply(control.res, filterDE)
fertilised.res.filter <- lapply(fertilised.res, filterDE)
combined.res.filter <- lapply(combined.res, filterDE)It is a good practice to do a check and see if the filtering was correct
lapply(control.res.filter, function(x) print(all(abs(x$log2FoldChange)>0.5 & x$padj<0.01)) )
lapply(fertilised.res.filter, function(x) print(all(abs(x$log2FoldChange)>0.5 & x$padj<0.01)) )
lapply(combined.res.filter, function(x) print(all(abs(x$log2FoldChange)>0.5 & x$padj<0.01)) )4.4 Plot DE genes
We can plot the results as positive and negative bars to reflect the amount of genes up or down regulated in each comparition For that we create a couple more vector to present the results
In order to get the results by week, and then treatment. 19C, 19F, 20C, …
mixVector <- c(rbind(controlVector, fertilisedVector))And to do the same by treatment. 19C, 20C, …, 41C, 19F, 20F, …
concatVector <- c(cbind(controlVector, fertilisedVector))4.4.1 Control week+1 vs week plot
plotUpAndDown(control.res.filter)
4.4.2 Fertilised week+1 vs week plot
plotUpAndDown(fertilised.res.filter)
4.4.3 Fertilised vs Control per week plot
plotUpAndDown(combined.res.filter)
4.5 DE Fertilisation vs Control
design(ddsMatrix) <- ~Treatment
ddsFungiTreatment <- DESeq(ddsMatrix)## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 43 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testingresFungiTreatment <- list( FertilisedvsControl = results(ddsFungiTreatment ,
name= "Treatment_F_vs_C",
filter = rowMedians(counts(ddsFungiTreatment )),
parallel = FALSE)
)
save(ddsFungiTreatment, resFungiTreatment, file=file.path(projectFolder, "DE", "ddsTreatment.RData"))
de4network(resFungiTreatment, file.path(deFolder,"deFvsC.tsv"))## [1] "FertilisedvsControl_lfc"
## [1] "FertilisedvsControl_padj"
## [1] TRUE## genes FertilisedvsControl_lfc FertilisedvsControl_padj
## 1 K00002 0.3977140007 9.386642e-04
## 2 K00003 -0.0683180439 4.192241e-01
## 3 K00004 1.0782744475 9.286047e-09
## 4 K00006 0.8231104222 2.096286e-06
## 5 K00008 0.0454147911 5.016583e-01
## 6 K00009 -0.3181098784 3.154413e-02
## 7 K00010 1.6001954342 3.036209e-15
## 8 K00012 0.2836802490 2.657485e-03
## 9 K00013 0.5854733785 3.267681e-04
## 10 K00015 0.6566052018 2.620156e-07
## 11 K00016 1.4843939686 2.655526e-14
## 12 K00018 -2.2733893549 7.456802e-35
## 13 K00019 2.2050611198 8.842739e-08
## 14 K00020 -0.4622680042 9.613154e-07
## 15 K00021 -1.1219530598 4.141244e-09
## 16 K00022 1.0178720717 5.600087e-06
## 17 K00026 -0.0260528401 6.991519e-01
## 18 K00027 -0.5427889668 5.081623e-11
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## 1882 K09523 -0.3368491180 1.111629e-05
## 1883 K09527 0.1197500968 2.874612e-01
## 1884 K09528 -0.4119257931 2.047625e-14
## 1885 K09529 -0.6016518802 5.382576e-13
## 1886 K09531 -0.4689602284 9.834827e-02
## 1887 K09537 0.9496142730 2.446074e-07
## 1888 K09539 -0.5643694510 1.616594e-08
## 1889 K09540 0.3133377893 3.897443e-13
## 1890 K09548 -1.4361138918 1.241244e-38
## 1891 K09549 -0.7183668493 1.996189e-13
## 1892 K09550 -0.1825267668 9.845752e-02
## 1893 K09553 -0.0681455101 4.332482e-01
## 1894 K09554 -0.2122928482 9.002815e-04
## 1895 K09561 0.7575129659 1.169611e-04
## 1896 K09564 -0.1440293871 1.597272e-01
## 1897 K09565 -1.4809179824 3.168666e-06
## 1898 K09566 -0.7680632616 4.911057e-04
## 1899 K09567 -0.6571464756 1.235765e-07
## 1900 K09568 -0.0737795494 5.217317e-01
## 1901 K09569 0.2911785464 1.379103e-02
## 1902 K09577 0.2813753144 1.906268e-02
## 1903 K09578 -0.5069055067 1.730610e-11
## 1904 K09579 0.0783219565 4.026994e-01
## 1905 K09580 0.5014901206 1.215602e-18
## 1906 K09584 0.2626740634 1.374064e-06
## 1907 K09595 0.9847722641 6.279464e-11
## 1908 K09602 0.0246003691 7.941581e-01
## 1909 K09611 -0.6016744669 1.162971e-11
## 1910 K09613 -1.0386975319 1.242741e-27
## 1911 K09645 0.6652300695 6.865781e-03
## 1912 K09647 1.0466350981 1.131766e-05
## 1913 K09648 -1.2234131343 9.831391e-14
## 1914 K09650 -0.0552904902 4.438480e-01
## 1915 K09658 -0.4916206548 1.621772e-03
## 1916 K09659 1.5068508501 2.428472e-08
## 1917 K09660 0.2371989838 1.725759e-03
## 1918 K09680 -0.6730771291 3.724947e-05
## 1919 K09699 0.2304547384 1.442340e-02
## 1920 K09702 1.4151729781 1.345942e-06
## 1921 K09704 0.7788692374 3.353010e-07
## 1922 K09705 -0.6235003197 2.472411e-03
## 1923 K09780 0.6480431982 2.135703e-03
## 1924 K09827 -0.4867932671 1.340521e-05
## 1925 K09829 -1.4072794454 3.641179e-23
## 1926 K09831 0.1690301747 2.937199e-02
## 1927 K09880 1.1808915047 3.960410e-08
## 1928 K09885 1.2101074141 2.820434e-11
## 1929 K09935 0.2510175634 1.229537e-01
## 1930 K09955 0.8679121761 1.021447e-04
## 1931 K09958 0.8027759152 5.306586e-08
## 1932 K09983 1.6254206261 2.050795e-11
## 1933 K10080 1.2762892748 8.085997e-11
## 1934 K10082 0.2216371378 1.255836e-06
## 1935 K10084 0.1266159565 6.259979e-02
## 1936 K10088 -0.4714982959 1.031969e-07
## 1937 K10089 0.5623981211 2.077119e-05
## 1938 K10112 2.8239759040 1.000000e+00
## 1939 K10134 -0.1652438548 7.444671e-01
## 1940 K10158 0.4449565409 2.350923e-02
## 1941 K10245 0.6453240503 1.694089e-16
## 1942 K10246 0.6425171244 2.079739e-16
## 1943 K10251 -0.2634999164 3.566994e-04
## 1944 K10253 0.1717367110 2.334536e-01
## 1945 K10256 0.3000590916 3.185306e-04
## 1946 K10258 -1.0070682988 6.989708e-24
## 1947 K10259 0.1632200643 1.672042e-03
## 1948 K10262 0.4263470803 1.000000e+00
## 1949 K10268 0.2246896956 1.030720e-01
## 1950 K10273 1.1210448100 8.106824e-13
## 1951 K10276 -0.4055334579 2.128004e-08
## 1952 K10277 -0.0992121810 3.831215e-02
## 1953 K10295 0.0689408341 4.722875e-01
## 1954 K10301 -0.2312545575 2.228553e-01
## 1955 K10352 -1.0340057852 1.625779e-17
## 1956 K10355 1.1896165136 2.041273e-06
## 1957 K10356 0.0147970549 7.307632e-01
## 1958 K10357 -0.0088305076 8.579670e-01
## 1959 K10364 -0.1173064032 5.771553e-02
## 1960 K10365 -0.3045670637 1.347404e-07
## 1961 K10367 -0.9383496009 1.000000e+00
## 1962 K10380 2.6116890494 2.375162e-10
## 1963 K10389 -0.0337019896 5.938231e-01
## 1964 K10392 -0.6393805043 4.308470e-23
## 1965 K10393 -0.3187112274 1.878256e-01
## 1966 K10395 -0.1548776344 3.215074e-02
## 1967 K10396 -0.3649605681 1.192402e-08
## 1968 K10398 0.0582511590 5.580311e-01
## 1969 K10401 -0.5533774847 3.370440e-06
## 1970 K10402 -0.3213056382 2.922508e-03
## 1971 K10403 -1.1247203795 1.979211e-17
## 1972 K10405 -0.5193937227 1.330299e-05
## 1973 K10407 1.6526509322 1.000000e+00
## 1974 K10413 0.2185850604 2.118927e-04
## 1975 K10415 -0.4998212912 3.133533e-14
## 1976 K10416 -0.3989144939 1.523731e-04
## 1977 K10418 -0.3147620061 6.655978e-05
## 1978 K10419 -1.1771566983 1.943004e-21
## 1979 K10421 -1.3639851790 1.264470e-15
## 1980 K10426 -0.2000918986 1.449192e-02
## 1981 K10427 -0.0837124996 3.277383e-01
## 1982 K10428 -0.3379610924 8.155925e-03
## 1983 K10436 0.2325101323 9.108049e-05
## 1984 K10437 0.0123106109 9.428792e-01
## 1985 K10438 1.6970293470 1.268211e-07
## 1986 K10523 1.4813575784 1.000000e+00
## 1987 K10524 0.0779528918 3.346683e-01
## 1988 K10531 0.7647657262 4.856543e-04
## 1989 K10534 -0.1154820305 5.984724e-01
## 1990 K10563 0.5648293314 6.638960e-03
## 1991 K10570 1.0672156558 3.172815e-08
## 1992 K10572 -0.4406767244 1.546779e-01
## 1993 K10573 -0.2519995471 4.371308e-04
## 1994 K10574 -0.2519995471 4.371308e-04
## 1995 K10575 -0.2049677842 2.778322e-03
## 1996 K10576 -0.3121603584 3.165321e-08
## 1997 K10577 -0.5497937618 1.558347e-07
## 1998 K10578 -0.6248271206 1.354218e-11
## 1999 K10579 -0.4277956494 5.780098e-08
## 2000 K10580 -0.2121923622 1.663712e-05
## 2001 K10581 0.3232790406 2.620816e-04
## 2002 K10582 -0.1679509037 4.145385e-02
## 2003 K10583 -0.1684201764 8.174011e-02
## 2004 K10585 1.2343849706 2.017153e-15
## 2005 K10586 -0.2152302541 2.978121e-01
## 2006 K10589 -0.0123161476 8.651418e-01
## 2007 K10590 -0.7664634518 4.741562e-32
## 2008 K10591 0.2567628521 4.511894e-10
## 2009 K10592 0.0250886340 6.240884e-01
## 2010 K10597 -0.1153143084 1.987341e-03
## 2011 K10598 -0.4872500077 2.294829e-10
## 2012 K10599 -0.5295382237 1.370783e-17
## 2013 K10601 -0.2765750089 2.653679e-05
## 2014 K10609 -0.6862053325 1.063567e-09
## 2015 K10610 -0.4889931387 9.743802e-06
## 2016 K10625 -1.0306300166 9.804769e-40
## 2017 K10627 0.9523820755 2.915017e-06
## 2018 K10631 -1.6696837444 1.393615e-30
## 2019 K10632 -0.0442069665 5.013574e-01
## 2020 K10638 -0.4665626432 2.410388e-03
## 2021 K10639 -2.0705891041 2.330116e-25
## 2022 K10643 0.0281784692 6.991519e-01
## 2023 K10644 -0.3849536702 4.559188e-05
## 2024 K10645 0.3740993759 1.000000e+00
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## 2027 K10666 1.4556477391 1.774540e-15
## 2028 K10669 -0.0908393642 4.897911e-01
## 2029 K10675 1.2149753398 6.540203e-05
## 2030 K10683 0.3970335874 3.481661e-01
## 2031 K10684 0.1366645161 5.616566e-02
## 2032 K10685 -0.0812880825 1.828143e-01
## 2033 K10686 -0.7399750229 1.832733e-17
## 2034 K10688 -1.0152793497 1.107448e-27
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## 2037 K10703 0.3950114023 3.980721e-06
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## 4078 K22262 -0.0243009017 7.299782e-01
## 4079 K22276 0.8236780612 1.765983e-05
## 4080 K22277 -0.3001328039 2.229995e-01
## 4081 K22278 -0.2680350041 2.761479e-01
## 4082 K22282 1.7643654804 1.000000e+00
## 4083 K22285 1.4305039833 6.408478e-43
## 4084 K22314 0.0068773852 9.481052e-01
## 4085 K22315 -0.3164938505 1.554788e-03
## 4086 K22337 -0.3387258031 3.273967e-06
## 4087 K22377 0.5251387235 3.475357e-05
## 4088 K22381 0.0790741689 4.069049e-01
## 4089 K22382 -0.2118631626 5.578792e-04
## 4090 K22384 0.1174116532 9.526797e-02
## 4091 K22386 -0.1353952919 4.015341e-01
## 4092 K22390 1.2194384174 1.595809e-06
## 4093 K22399 0.3117730190 8.589283e-02
## 4094 K22418 -0.1156836775 4.826955e-01
## 4095 K22419 1.1045509347 6.827131e-04
## 4096 K22438 -0.5208652713 1.168592e-07
## 4097 K22445 1.8366892623 1.000000e+00
## 4098 K22470 -0.1159126621 4.842952e-01
## 4099 K22483 2.8643531237 1.124408e-11
## 4100 K22484 0.5646779115 6.700634e-14
## 4101 K22485 0.6681192170 7.900538e-03
## 4102 K22494 -0.4407656809 2.915883e-02
## 4103 K22496 -1.0408464827 1.426251e-11
## 4104 K22503 0.0001685481 9.979437e-01resFungiTreatment.filter <- lapply(resFungiTreatment, filterDE)## [1] "Filtering by: padj = 0.01 and lfc= 0.5"plotUpAndDown(resFungiTreatment.filter)
4.6 Top genes
To check the top genes in each comparition we create a dot plot for the top 6 genes with two lines (read and blue) that highligths the comparition pair that we want to check and store it as a PDF
plotTop(control.res.filter, dds, plotGroup=c('Treatment','Week'), infoVector=concatVector, name = file.path(deFolder,"controlFilter.pdf"))
plotTop(fertilised.res.filter, dds, plotGroup=c('Treatment','Week'), infoVector=concatVector, name = file.path(deFolder,"fertilisedFilter.pdf"))
plotTop(combined.res.filter, dds, plotGroup=c('Week','Treatment'), infoVector=mixVector, name = file.path(deFolder,"combinedFilter.pdf"))5 Results export
5.1 Background for enrichment
We need to extract the names of all the genes that at least have 1 count across all samples to establish a background needed for future enrichment steps
write.table(colnames(t(assay(dds))), file=file.path(deFolder,"background.txt"), row.names = F,col.names = F, quote = F )5.2 Data for networks
For a co-expression network construction we need the vst data after doing a zeroMAD (Mean Decrease Accuracy) cleanup. That will remove genes with zero or almost zero expression. For the network construction with Seidr we need a headless files with the data and a file only with the gene names
5.2.1 Combined
vsdCombined <- vst(dds, blind=FALSE)
combinedData <- t(assay(vsdCombined))
combinedData <- combinedData[,which(colMads(as.matrix(combinedData)) > 0)]
save(combinedData, file=file.path(deFolder,"combinedVsdData.RData"))
write.table(combinedData, file =file.path(deFolder,"fungi2011Combined.tsv"), sep='\t', row.names=FALSE, col.names=FALSE)
writeLines(colnames(combinedData), con=file.path(deFolder,"fungi2011CombinedNames.txt"))5.2.2 Control & fertilised
In order to make this individual networks, we need to specify a new design to obtain the vst data using model awareness. In this case, the model should be treatment.
ddsSplit <- dds
design(ddsSplit) <- ~Treatment
vsdSplit <- vst(ddsSplit, blind=F)
vsdSplitData <- t(assay(vsdSplit))
controlData <- vsdSplitData[grep("C",rownames(vsdSplitData)),]
controlData <- controlData[,which(colMads(as.matrix(controlData)) > 0)]
fertilisedData <- vsdSplitData[grep("F",rownames(vsdSplitData)),]
fertilisedData <- fertilisedData[,which(colMads(as.matrix(fertilisedData)) > 0)]
save(controlData, file=file.path(deFolder,"controlVsdData.RData"))
write.table(controlData, file = file.path(deFolder,"fungi2011Control.tsv"), sep='\t', row.names=FALSE, col.names=FALSE)
writeLines(colnames(controlData), con=file.path(deFolder,"fungi2011ControlNames.txt"))
save(fertilisedData, file=file.path(deFolder,"fertilisedVsdData.RData"))
write.table(fertilisedData, file = file.path(deFolder,"fungi2011Fertilised.tsv"), sep='\t', row.names=FALSE, col.names=FALSE)
writeLines(colnames(fertilisedData), con=file.path(deFolder,"fungi2011FertilisedNames.txt"))5.3 DE results
For downstream analysis we export each set of results to a tsv file containing the padj and log2foldchange values for each comparition. We export the results unfiltered
5.4 DE enrichment
We set the background
background <- read.table(file.path(deFolder, "background.txt"), sep='\t', header=F, stringsAsFactors = F)[,1] Now we use gopher to obtain the enrichment results for up and down expressed genes
control.res.enr <- getDEenrichment(control.res.filter, background)## Loading required package: tidyr##
## Attaching package: 'tidyr'## The following object is masked from 'package:S4Vectors':
##
## expand## Loading required package: tibble## Loading required package: jsonlite## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04966 map04966 4104 10 14 map04966
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04150 map04150 4104 46 14 map04150
## 3 https://www.kegg.jp/dbget-bin/www_bget?map05110 map05110 4104 20 14 map05110
## 4 https://www.kegg.jp/dbget-bin/www_bget?map04721 map04721 4104 24 14 map04721
## 5 https://www.kegg.jp/dbget-bin/www_bget?map04145 map04145 4104 36 14 map04145
## 6 https://www.kegg.jp/dbget-bin/www_bget?map05120 map05120 4104 16 14 map05120
## 7 https://www.kegg.jp/dbget-bin/www_bget?map05165 map05165 4104 50 14 map05165
## 8 https://www.kegg.jp/dbget-bin/www_bget?map05323 map05323 4104 13 14 map05323
## nt padj pval
## 1 2 0.01155213 0.0004788439
## 2 2 0.04106870 0.0102671761
## 3 2 0.01387911 0.0019827299
## 4 2 0.01600369 0.0028578011
## 5 2 0.02973819 0.0063724699
## 6 2 0.01177920 0.0012620575
## 7 2 0.04220208 0.0120577373
## 8 2 0.01155213 0.0008251521
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03018 map03018 4104 55 2 map03018
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04144 map04144 4104 74 2 map04144
## nt padj pval
## 1 1 0.03574157 0.02662674
## 2 1 0.03574157 0.03574157
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00660 map00660 4104 5 29 map00660
## 2 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 29 map03010
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00290 map00290 4104 10 29 map00290
## nt padj pval
## 1 2 1.070784e-02 4.759042e-04
## 2 9 1.736425e-06 3.858723e-08
## 3 2 3.142617e-02 2.095078e-03
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00300 map00300 4104 11 14 map00300
## nt padj pval
## 1 2 0.03271032 0.0005841128
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03008 map03008 4104 69 2 map03008
## 2 https://www.kegg.jp/dbget-bin/www_bget?map00970 map00970 4104 26 2 map00970
## nt padj pval
## 1 1 0.03334709 0.03334709
## 2 1 0.02526393 0.01263196
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00250 map00250 4104 30 4 map00250
## 2 https://www.kegg.jp/dbget-bin/www_bget?map00310 map00310 4104 25 4 map00310
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00100 map00100 4104 19 4 map00100
## 4 https://www.kegg.jp/dbget-bin/www_bget?map00300 map00300 4104 11 4 map00300
## 5 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 4 map01110
## 6 https://www.kegg.jp/dbget-bin/www_bget?map01130 map01130 4104 220 4 map01130
## nt padj pval
## 1 1 0.048218624 0.0289311745
## 2 1 0.048218624 0.0241534768
## 3 1 0.045992482 0.0183969928
## 4 1 0.035607032 0.0106821095
## 5 3 0.007391736 0.0014783472
## 6 3 0.005841068 0.0005841068
##
## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00230 map00230 4104 52 110
## 2 https://www.kegg.jp/dbget-bin/www_bget?map01130 map01130 4104 220 110
## name nt padj pval
## 1 map00230 8 0.009310594 5.819121e-05
## 2 map01130 16 0.016536925 2.067116e-04
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00020 map00020 4104 21 7 map00020
## nt padj pval
## 1 2 0.007220625 0.0005157589
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00730 map00730 4104 14 2 map00730
## nt padj pval
## 1 1 0.04087082 0.006811804
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00250 map00250 4104 30 17 map00250
## 2 https://www.kegg.jp/dbget-bin/www_bget?map02020 map02020 4104 19 17 map02020
## 3 https://www.kegg.jp/dbget-bin/www_bget?map04612 map04612 4104 11 17 map04612
## nt padj pval
## 1 3 0.01118876 0.0002237752
## 2 2 0.04416745 0.0026500471
## 3 2 0.02172837 0.0008691349
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00900 map00900 4104 20 2 map00900
## nt padj pval
## 1 1 0.04862011 0.009724022
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00760 map00760 4104 18 4 map00760
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04211 map04211 4104 19 4 map04211
## 3 https://www.kegg.jp/dbget-bin/www_bget?map04213 map04213 4104 22 4 map04213
## 4 https://www.kegg.jp/dbget-bin/www_bget?map04136 map04136 4104 23 4 map04136
## 5 https://www.kegg.jp/dbget-bin/www_bget?map04621 map04621 4104 21 4 map04621
## 6 https://www.kegg.jp/dbget-bin/www_bget?map04137 map04137 4104 19 4 map04137
## 7 https://www.kegg.jp/dbget-bin/www_bget?map04216 map04216 4104 9 4 map04216
## 8 https://www.kegg.jp/dbget-bin/www_bget?map04622 map04622 4104 9 4 map04622
## 9 https://www.kegg.jp/dbget-bin/www_bget?map05131 map05131 4104 21 4 map05131
## nt padj pval
## 1 1 0.04447494 0.017435108
## 2 1 0.04447494 0.018396993
## 3 1 0.04447494 0.021278409
## 4 1 0.04447494 0.022237470
## 5 1 0.04447494 0.020318643
## 6 1 0.04447494 0.018396993
## 7 1 0.04447494 0.008746304
## 8 1 0.04447494 0.008746304
## 9 1 0.04447494 0.020318643
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00650 map00650 4104 18 6 map00650
## 2 https://www.kegg.jp/dbget-bin/www_bget?map00072 map00072 4104 5 6 map00072
## 3 https://www.kegg.jp/dbget-bin/www_bget?map04020 map04020 4104 14 6 map04020
## 4 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 6 map01110
## 5 https://www.kegg.jp/dbget-bin/www_bget?map01130 map01130 4104 220 6 map01130
## 6 https://www.kegg.jp/dbget-bin/www_bget?map00900 map00900 4104 20 6 map00900
## 7 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 6 map01100
## 8 https://www.kegg.jp/dbget-bin/www_bget?map04976 map04976 4104 8 6 map04976
## 9 https://www.kegg.jp/dbget-bin/www_bget?map04972 map04972 4104 10 6 map04972
## 10 https://www.kegg.jp/dbget-bin/www_bget?map04022 map04022 4104 19 6 map04022
## 11 https://www.kegg.jp/dbget-bin/www_bget?map00910 map00910 4104 16 6 map00910
## 12 https://www.kegg.jp/dbget-bin/www_bget?map00770 map00770 4104 18 6 map00770
## nt padj pval
## 1 1 0.043501769 0.0260446171
## 2 1 0.034637678 0.0072921428
## 3 1 0.043501769 0.0203063410
## 4 3 0.034637678 0.0066121997
## 5 3 0.025594777 0.0026941871
## 6 2 0.006356698 0.0003345631
## 7 4 0.043501769 0.0248805060
## 8 1 0.043501769 0.0116461186
## 9 1 0.043501769 0.0145399188
## 10 1 0.043501769 0.0274748012
## 11 1 0.043501769 0.0231789904
## 12 1 0.043501769 0.0260446171
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00900 map00900 4104 20 11 map00900
## 2 https://www.kegg.jp/dbget-bin/www_bget?map00232 map00232 4104 2 11 map00232
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00280 map00280 4104 27 11 map00280
## 4 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 11 map01100
## 5 https://www.kegg.jp/dbget-bin/www_bget?map00072 map00072 4104 5 11 map00072
## nt padj pval
## 1 2 0.01878960 0.001208912
## 2 1 0.02275489 0.005354091
## 3 2 0.01878960 0.002210541
## 4 7 0.02120907 0.003742776
## 5 1 0.04534368 0.013336377fertilised.res.enr <- getDEenrichment(fertilised.res.filter, background)## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04216 map04216 4104 9 43 map04216
## 2 https://www.kegg.jp/dbget-bin/www_bget?map01130 map01130 4104 220 43 map01130
## 3 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 43 map01100
## 4 https://www.kegg.jp/dbget-bin/www_bget?map04217 map04217 4104 24 43 map04217
## 5 https://www.kegg.jp/dbget-bin/www_bget?map00260 map00260 4104 39 43 map00260
## 6 https://www.kegg.jp/dbget-bin/www_bget?map00500 map00500 4104 32 43 map00500
## 7 https://www.kegg.jp/dbget-bin/www_bget?map00040 map00040 4104 20 43 map00040
## 8 https://www.kegg.jp/dbget-bin/www_bget?map00051 map00051 4104 31 43 map00051
## 9 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 43 map01110
## nt padj pval
## 1 2 0.0301096071 3.684909e-03
## 2 9 0.0111401756 3.536564e-04
## 3 23 0.0004495926 7.136390e-06
## 4 3 0.0195361687 1.860587e-03
## 5 4 0.0132448173 6.586333e-04
## 6 3 0.0301096071 4.301372e-03
## 7 3 0.0135955531 1.079012e-03
## 8 3 0.0301096071 3.926591e-03
## 9 10 0.0132448173 8.409408e-04
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04068 map04068 4104 22 26 map04068
## nt padj pval
## 1 3 0.02825333 0.0003210606
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 36 map01100
## nt padj pval
## 1 19 0.003822103 5.791065e-05
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00591 map00591 4104 6 29 map00591
## 2 https://www.kegg.jp/dbget-bin/www_bget?map00260 map00260 4104 39 29 map00260
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00430 map00430 4104 7 29 map00430
## nt padj pval
## 1 2 0.02377580 0.0007107273
## 2 3 0.03910977 0.0024443608
## 3 2 0.02377580 0.0009906584
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04213 map04213 4104 22 31 map04213
## nt padj pval
## 1 3 0.03818482 0.0005454975
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 141
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04216 map04216 4104 9 141
## name nt padj pval
## 1 map03010 23 1.879880e-10 1.261664e-12
## 2 map04216 4 1.096099e-02 1.471274e-04
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map05132 map05132 4104 19 269
## 2 https://www.kegg.jp/dbget-bin/www_bget?map05110 map05110 4104 20 269
## 3 https://www.kegg.jp/dbget-bin/www_bget?map04380 map04380 4104 10 269
## 4 https://www.kegg.jp/dbget-bin/www_bget?map04010 map04010 4104 31 269
## 5 https://www.kegg.jp/dbget-bin/www_bget?map04658 map04658 4104 5 269
## 6 https://www.kegg.jp/dbget-bin/www_bget?map03050 map03050 4104 37 269
## 7 https://www.kegg.jp/dbget-bin/www_bget?map04370 map04370 4104 15 269
## 8 https://www.kegg.jp/dbget-bin/www_bget?map05120 map05120 4104 16 269
## 9 https://www.kegg.jp/dbget-bin/www_bget?map05323 map05323 4104 13 269
## 10 https://www.kegg.jp/dbget-bin/www_bget?map05152 map05152 4104 27 269
## 11 https://www.kegg.jp/dbget-bin/www_bget?map04013 map04013 4104 20 269
## 12 https://www.kegg.jp/dbget-bin/www_bget?map04145 map04145 4104 36 269
## 13 https://www.kegg.jp/dbget-bin/www_bget?map05131 map05131 4104 21 269
## 14 https://www.kegg.jp/dbget-bin/www_bget?map05322 map05322 4104 8 269
## 15 https://www.kegg.jp/dbget-bin/www_bget?map04144 map04144 4104 74 269
## 16 https://www.kegg.jp/dbget-bin/www_bget?map04966 map04966 4104 10 269
## 17 https://www.kegg.jp/dbget-bin/www_bget?map04310 map04310 4104 22 269
## name nt padj pval
## 1 map05132 7 4.018068e-03 1.222890e-04
## 2 map05110 7 5.109130e-03 1.777089e-04
## 3 map04380 4 3.974810e-02 2.765085e-03
## 4 map04010 7 4.370939e-02 3.230694e-03
## 5 map04658 3 3.974810e-02 2.522603e-03
## 6 map03050 14 6.933776e-06 3.014685e-08
## 7 map04370 5 3.588659e-02 2.028373e-03
## 8 map05120 8 1.912915e-04 2.495107e-06
## 9 map05323 5 2.229418e-02 9.693120e-04
## 10 map05152 7 2.621512e-02 1.367745e-03
## 11 map04013 6 2.621512e-02 1.328251e-03
## 12 map04145 12 1.715277e-04 1.491545e-06
## 13 map05131 8 1.358127e-03 2.952451e-05
## 14 map05322 5 2.125900e-03 5.545826e-05
## 15 map04144 16 9.043658e-04 1.572810e-05
## 16 map04966 4 3.974810e-02 2.765085e-03
## 17 map04310 7 8.915669e-03 3.488740e-04
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04391 map04391 4104 11 473
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04390 map04390 4104 16 473
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00020 map00020 4104 21 473
## 4 https://www.kegg.jp/dbget-bin/www_bget?map05120 map05120 4104 16 473
## 5 https://www.kegg.jp/dbget-bin/www_bget?map01130 map01130 4104 220 473
## 6 https://www.kegg.jp/dbget-bin/www_bget?map05323 map05323 4104 13 473
## 7 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 473
## 8 https://www.kegg.jp/dbget-bin/www_bget?map00010 map00010 4104 32 473
## 9 https://www.kegg.jp/dbget-bin/www_bget?map05110 map05110 4104 20 473
## 10 https://www.kegg.jp/dbget-bin/www_bget?map00740 map00740 4104 11 473
## 11 https://www.kegg.jp/dbget-bin/www_bget?map05322 map05322 4104 8 473
## 12 https://www.kegg.jp/dbget-bin/www_bget?map00500 map00500 4104 32 473
## 13 https://www.kegg.jp/dbget-bin/www_bget?map05012 map05012 4104 64 473
## 14 https://www.kegg.jp/dbget-bin/www_bget?map01230 map01230 4104 103 473
## 15 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 473
## 16 https://www.kegg.jp/dbget-bin/www_bget?map05165 map05165 4104 50 473
## 17 https://www.kegg.jp/dbget-bin/www_bget?map04966 map04966 4104 10 473
## 18 https://www.kegg.jp/dbget-bin/www_bget?map04721 map04721 4104 24 473
## 19 https://www.kegg.jp/dbget-bin/www_bget?map04145 map04145 4104 36 473
## 20 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 473
## 21 https://www.kegg.jp/dbget-bin/www_bget?map05010 map05010 4104 62 473
## 22 https://www.kegg.jp/dbget-bin/www_bget?map04932 map04932 4104 51 473
## 23 https://www.kegg.jp/dbget-bin/www_bget?map00190 map00190 4104 77 473
## 24 https://www.kegg.jp/dbget-bin/www_bget?map04152 map04152 4104 32 473
## 25 https://www.kegg.jp/dbget-bin/www_bget?map01200 map01200 4104 87 473
## 26 https://www.kegg.jp/dbget-bin/www_bget?map03050 map03050 4104 37 473
## 27 https://www.kegg.jp/dbget-bin/www_bget?map05016 map05016 4104 76 473
## 28 https://www.kegg.jp/dbget-bin/www_bget?map00052 map00052 4104 17 473
## name nt padj pval
## 1 map04391 5 4.884303e-02 5.084033e-03
## 2 map04390 7 1.647814e-02 1.163883e-03
## 3 map00020 8 2.050877e-02 1.524816e-03
## 4 map05120 7 1.647814e-02 1.163883e-03
## 5 map01130 50 6.174569e-05 9.181515e-07
## 6 map05323 7 4.897551e-03 2.381893e-04
## 7 map01100 148 6.174569e-05 8.313572e-07
## 8 map00010 10 2.582951e-02 2.304491e-03
## 9 map05110 9 4.244757e-03 1.735774e-04
## 10 map00740 5 4.884303e-02 5.084033e-03
## 11 map05322 5 1.486239e-02 8.287580e-04
## 12 map00500 14 1.782898e-04 3.976723e-06
## 13 map05012 18 4.701824e-03 2.097468e-04
## 14 map01230 26 2.007833e-03 6.717658e-05
## 15 map01110 62 8.800766e-05 1.635830e-06
## 16 map05165 14 1.647814e-02 1.104483e-03
## 17 map04966 7 7.654430e-04 2.276410e-05
## 18 map04721 9 1.486311e-02 8.840511e-04
## 19 map04145 11 2.182166e-02 1.723585e-03
## 20 map03010 44 3.820664e-12 1.420321e-14
## 21 map05010 18 3.612565e-03 1.342961e-04
## 22 map04932 13 4.244762e-02 4.102744e-03
## 23 map00190 23 3.641378e-04 9.475706e-06
## 24 map04152 10 2.582951e-02 2.304491e-03
## 25 map01200 19 4.244762e-02 3.963122e-03
## 26 map03050 17 1.999162e-05 1.486365e-07
## 27 map05016 20 4.897551e-03 2.548912e-04
## 28 map00052 7 2.182166e-02 1.784671e-03
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04122 map04122 4104 11 60 map04122
## nt padj pval
## 1 3 0.0302234 0.0004510955
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03450 map03450 4104 10 42 map03450
## nt padj pval
## 1 3 0.01024402 0.0001138225
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04142 map04142 4104 34 11 map04142
## 2 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 11 map01100
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00270 map00270 4104 40 11 map00270
## 4 https://www.kegg.jp/dbget-bin/www_bget?map00520 map00520 4104 37 11 map00520
## 5 https://www.kegg.jp/dbget-bin/www_bget?map00603 map00603 4104 2 11 map00603
## nt padj pval
## 1 2 0.02784127 0.0034970721
## 2 8 0.01317296 0.0005066522
## 3 2 0.02784127 0.0048197271
## 4 2 0.02784127 0.0041334149
## 5 1 0.02784127 0.0053540912
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map05031 map05031 4104 11 5 map05031
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04728 map04728 4104 23 5 map04728
## 3 https://www.kegg.jp/dbget-bin/www_bget?map04726 map04726 4104 18 5 map04726
## 4 https://www.kegg.jp/dbget-bin/www_bget?map03030 map03030 4104 32 5 map03030
## 5 https://www.kegg.jp/dbget-bin/www_bget?map00561 map00561 4104 26 5 map00561
## 6 https://www.kegg.jp/dbget-bin/www_bget?map00950 map00950 4104 9 5 map00950
## 7 https://www.kegg.jp/dbget-bin/www_bget?map05034 map05034 4104 27 5 map05034
## 8 https://www.kegg.jp/dbget-bin/www_bget?map00350 map00350 4104 23 5 map00350
## 9 https://www.kegg.jp/dbget-bin/www_bget?map00380 map00380 4104 29 5 map00380
## 10 https://www.kegg.jp/dbget-bin/www_bget?map05030 map05030 4104 7 5 map05030
## 11 https://www.kegg.jp/dbget-bin/www_bget?map00901 map00901 4104 5 5 map00901
## 12 https://www.kegg.jp/dbget-bin/www_bget?map00360 map00360 4104 18 5 map00360
## 13 https://www.kegg.jp/dbget-bin/www_bget?map00965 map00965 4104 4 5 map00965
## nt padj pval
## 1 1 0.04267641 0.013336377
## 2 1 0.04646977 0.027722479
## 3 1 0.04646977 0.021748808
## 4 1 0.04726342 0.038401529
## 5 1 0.04646977 0.031292650
## 6 1 0.04267641 0.010922227
## 7 1 0.04646977 0.032480374
## 8 1 0.04646977 0.027722479
## 9 1 0.04646977 0.034852326
## 10 1 0.04267641 0.008503353
## 11 1 0.04267641 0.006079749
## 12 1 0.04646977 0.021748808
## 13 1 0.04267641 0.004866171
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 56 map03010
## nt padj pval
## 1 28 1.114966e-28 1.922355e-30
##
## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04966 map04966 4104 10 249
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04145 map04145 4104 36 249
## 3 https://www.kegg.jp/dbget-bin/www_bget?map04141 map04141 4104 81 249
## 4 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 249
## 5 https://www.kegg.jp/dbget-bin/www_bget?map00190 map00190 4104 77 249
## 6 https://www.kegg.jp/dbget-bin/www_bget?map00020 map00020 4104 21 249
## 7 https://www.kegg.jp/dbget-bin/www_bget?map05152 map05152 4104 27 249
## 8 https://www.kegg.jp/dbget-bin/www_bget?map01130 map01130 4104 220 249
## 9 https://www.kegg.jp/dbget-bin/www_bget?map05110 map05110 4104 20 249
## 10 https://www.kegg.jp/dbget-bin/www_bget?map05120 map05120 4104 16 249
## name nt padj pval
## 1 map04966 4 0.048378092 2.076313e-03
## 2 map04145 10 0.004103183 3.522045e-05
## 3 map04141 13 0.039127132 1.009333e-03
## 4 map01110 38 0.001684627 7.230161e-06
## 5 map00190 12 0.048378092 2.037601e-03
## 6 map00020 6 0.039127132 1.175493e-03
## 7 map05152 7 0.039127132 8.647272e-04
## 8 map01130 26 0.039127132 6.560781e-04
## 9 map05110 6 0.039127132 8.839453e-04
## 10 map05120 5 0.048378092 1.983177e-03
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04110 map04110 4104 53 277 map04110
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04914 map04914 4104 25 277 map04914
## nt padj pval
## 1 13 0.005353875 3.304861e-05
## 2 8 0.012402125 1.531127e-04combined.res.enr <- getDEenrichment(combined.res.filter, background)## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04392 map04392 4104 9 2 map04392
## 2 https://www.kegg.jp/dbget-bin/www_bget?map00020 map00020 4104 21 2 map00020
## nt padj pval
## 1 1 0.03505351 0.004381689
## 2 1 0.04083590 0.010208976
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04721 map04721 4104 24 46
## 2 https://www.kegg.jp/dbget-bin/www_bget?map05145 map05145 4104 12 46
## 3 https://www.kegg.jp/dbget-bin/www_bget?map05142 map05142 4104 9 46
## 4 https://www.kegg.jp/dbget-bin/www_bget?map05140 map05140 4104 6 46
## 5 https://www.kegg.jp/dbget-bin/www_bget?map05133 map05133 4104 8 46
## 6 https://www.kegg.jp/dbget-bin/www_bget?map05131 map05131 4104 21 46
## 7 https://www.kegg.jp/dbget-bin/www_bget?map05120 map05120 4104 16 46
## 8 https://www.kegg.jp/dbget-bin/www_bget?map05323 map05323 4104 13 46
## 9 https://www.kegg.jp/dbget-bin/www_bget?map04657 map04657 4104 11 46
## 10 https://www.kegg.jp/dbget-bin/www_bget?map04621 map04621 4104 21 46
## 11 https://www.kegg.jp/dbget-bin/www_bget?map04611 map04611 4104 20 46
## 12 https://www.kegg.jp/dbget-bin/www_bget?map04261 map04261 4104 15 46
## 13 https://www.kegg.jp/dbget-bin/www_bget?map04668 map04668 4104 11 46
## 14 https://www.kegg.jp/dbget-bin/www_bget?map05231 map05231 4104 19 46
## 15 https://www.kegg.jp/dbget-bin/www_bget?map05230 map05230 4104 17 46
## 16 https://www.kegg.jp/dbget-bin/www_bget?map05226 map05226 4104 15 46
## 17 https://www.kegg.jp/dbget-bin/www_bget?map05224 map05224 4104 13 46
## 18 https://www.kegg.jp/dbget-bin/www_bget?map05223 map05223 4104 10 46
## 19 https://www.kegg.jp/dbget-bin/www_bget?map05221 map05221 4104 8 46
## 20 https://www.kegg.jp/dbget-bin/www_bget?map04068 map04068 4104 22 46
## 21 https://www.kegg.jp/dbget-bin/www_bget?map04012 map04012 4104 12 46
## 22 https://www.kegg.jp/dbget-bin/www_bget?map05166 map05166 4104 46 46
## 23 https://www.kegg.jp/dbget-bin/www_bget?map05163 map05163 4104 30 46
## 24 https://www.kegg.jp/dbget-bin/www_bget?map04960 map04960 4104 6 46
## 25 https://www.kegg.jp/dbget-bin/www_bget?map05014 map05014 4104 11 46
## 26 https://www.kegg.jp/dbget-bin/www_bget?map04921 map04921 4104 23 46
## 27 https://www.kegg.jp/dbget-bin/www_bget?map01521 map01521 4104 15 46
## 28 https://www.kegg.jp/dbget-bin/www_bget?map04933 map04933 4104 15 46
## 29 https://www.kegg.jp/dbget-bin/www_bget?map04660 map04660 4104 14 46
## 30 https://www.kegg.jp/dbget-bin/www_bget?map04140 map04140 4104 46 46
## 31 https://www.kegg.jp/dbget-bin/www_bget?map04013 map04013 4104 20 46
## 32 https://www.kegg.jp/dbget-bin/www_bget?map04966 map04966 4104 10 46
## 33 https://www.kegg.jp/dbget-bin/www_bget?map04659 map04659 4104 6 46
## 34 https://www.kegg.jp/dbget-bin/www_bget?map04730 map04730 4104 12 46
## 35 https://www.kegg.jp/dbget-bin/www_bget?map05212 map05212 4104 14 46
## 36 https://www.kegg.jp/dbget-bin/www_bget?map04014 map04014 4104 29 46
## 37 https://www.kegg.jp/dbget-bin/www_bget?map04658 map04658 4104 5 46
## 38 https://www.kegg.jp/dbget-bin/www_bget?map04145 map04145 4104 36 46
## 39 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 46
## 40 https://www.kegg.jp/dbget-bin/www_bget?map05170 map05170 4104 39 46
## 41 https://www.kegg.jp/dbget-bin/www_bget?map04724 map04724 4104 12 46
## 42 https://www.kegg.jp/dbget-bin/www_bget?map01522 map01522 4104 10 46
## 43 https://www.kegg.jp/dbget-bin/www_bget?map04915 map04915 4104 14 46
## 44 https://www.kegg.jp/dbget-bin/www_bget?map04720 map04720 4104 12 46
## 45 https://www.kegg.jp/dbget-bin/www_bget?map04071 map04071 4104 32 46
## 46 https://www.kegg.jp/dbget-bin/www_bget?map04662 map04662 4104 10 46
## 47 https://www.kegg.jp/dbget-bin/www_bget?map05211 map05211 4104 14 46
## 48 https://www.kegg.jp/dbget-bin/www_bget?map05110 map05110 4104 20 46
## 49 https://www.kegg.jp/dbget-bin/www_bget?map04625 map04625 4104 12 46
## 50 https://www.kegg.jp/dbget-bin/www_bget?map04914 map04914 4104 25 46
## 51 https://www.kegg.jp/dbget-bin/www_bget?map04725 map04725 4104 12 46
## 52 https://www.kegg.jp/dbget-bin/www_bget?map04912 map04912 4104 13 46
## 53 https://www.kegg.jp/dbget-bin/www_bget?map04010 map04010 4104 31 46
## 54 https://www.kegg.jp/dbget-bin/www_bget?map04218 map04218 4104 31 46
## 55 https://www.kegg.jp/dbget-bin/www_bget?map04062 map04062 4104 23 46
## 56 https://www.kegg.jp/dbget-bin/www_bget?map05167 map05167 4104 22 46
## 57 https://www.kegg.jp/dbget-bin/www_bget?map05132 map05132 4104 19 46
## 58 https://www.kegg.jp/dbget-bin/www_bget?map04370 map04370 4104 15 46
## 59 https://www.kegg.jp/dbget-bin/www_bget?map04371 map04371 4104 21 46
## 60 https://www.kegg.jp/dbget-bin/www_bget?map05152 map05152 4104 27 46
## 61 https://www.kegg.jp/dbget-bin/www_bget?map05219 map05219 4104 5 46
## 62 https://www.kegg.jp/dbget-bin/www_bget?map04360 map04360 4104 19 46
## 63 https://www.kegg.jp/dbget-bin/www_bget?map04072 map04072 4104 17 46
## 64 https://www.kegg.jp/dbget-bin/www_bget?map04380 map04380 4104 10 46
## 65 https://www.kegg.jp/dbget-bin/www_bget?map04620 map04620 4104 9 46
## 66 https://www.kegg.jp/dbget-bin/www_bget?map04320 map04320 4104 7 46
## 67 https://www.kegg.jp/dbget-bin/www_bget?map04150 map04150 4104 46 46
## 68 https://www.kegg.jp/dbget-bin/www_bget?map04214 map04214 4104 17 46
## 69 https://www.kegg.jp/dbget-bin/www_bget?map05161 map05161 4104 15 46
## 70 https://www.kegg.jp/dbget-bin/www_bget?map05216 map05216 4104 9 46
## 71 https://www.kegg.jp/dbget-bin/www_bget?map04540 map04540 4104 12 46
## 72 https://www.kegg.jp/dbget-bin/www_bget?map04550 map04550 4104 10 46
## 73 https://www.kegg.jp/dbget-bin/www_bget?map04664 map04664 4104 11 46
## 74 https://www.kegg.jp/dbget-bin/www_bget?map04015 map04015 4104 22 46
## 75 https://www.kegg.jp/dbget-bin/www_bget?map04722 map04722 4104 21 46
## 76 https://www.kegg.jp/dbget-bin/www_bget?map04650 map04650 4104 11 46
## 77 https://www.kegg.jp/dbget-bin/www_bget?map05218 map05218 4104 7 46
## 78 https://www.kegg.jp/dbget-bin/www_bget?map04916 map04916 4104 11 46
## 79 https://www.kegg.jp/dbget-bin/www_bget?map04917 map04917 4104 9 46
## 80 https://www.kegg.jp/dbget-bin/www_bget?map04926 map04926 4104 17 46
## 81 https://www.kegg.jp/dbget-bin/www_bget?map04210 map04210 4104 18 46
## 82 https://www.kegg.jp/dbget-bin/www_bget?map05205 map05205 4104 27 46
## 83 https://www.kegg.jp/dbget-bin/www_bget?map04022 map04022 4104 19 46
## 84 https://www.kegg.jp/dbget-bin/www_bget?map05210 map05210 4104 19 46
## 85 https://www.kegg.jp/dbget-bin/www_bget?map04726 map04726 4104 18 46
## 86 https://www.kegg.jp/dbget-bin/www_bget?map05213 map05213 4104 12 46
## 87 https://www.kegg.jp/dbget-bin/www_bget?map05214 map05214 4104 12 46
## 88 https://www.kegg.jp/dbget-bin/www_bget?map05165 map05165 4104 50 46
## 89 https://www.kegg.jp/dbget-bin/www_bget?map05215 map05215 4104 14 46
## 90 https://www.kegg.jp/dbget-bin/www_bget?map05220 map05220 4104 9 46
## name nt padj pval
## 1 map04721 3 0.0090496662 2.262417e-03
## 2 map05145 2 0.0187689187 7.553345e-03
## 3 map05142 2 0.0132749942 4.209145e-03
## 4 map05140 2 0.0075349143 1.791839e-03
## 5 map05133 2 0.0115053167 3.297255e-03
## 6 map05131 2 0.0415437552 2.254509e-02
## 7 map05120 4 0.0006034086 2.279910e-05
## 8 map05323 3 0.0021984656 3.485372e-04
## 9 map04657 2 0.0179254596 6.339492e-03
## 10 map04621 2 0.0415437552 2.254509e-02
## 11 map04611 2 0.0391748206 2.054289e-02
## 12 map04261 2 0.0257212506 1.176277e-02
## 13 map04668 2 0.0179254596 6.339492e-03
## 14 map05231 2 0.0359258298 1.862009e-02
## 15 map05230 2 0.0311820012 1.502060e-02
## 16 map05226 2 0.0257212506 1.176277e-02
## 17 map05224 2 0.0213762193 8.863310e-03
## 18 map05223 2 0.0158654722 5.223997e-03
## 19 map05221 2 0.0115053167 3.297255e-03
## 20 map04068 3 0.0075349143 1.748613e-03
## 21 map04012 2 0.0187689187 7.553345e-03
## 22 map05166 3 0.0304370792 1.429058e-02
## 23 map05163 4 0.0021984656 3.060430e-04
## 24 map04960 2 0.0075349143 1.791839e-03
## 25 map05014 2 0.0179254596 6.339492e-03
## 26 map04921 3 0.0081803024 1.995196e-03
## 27 map01521 2 0.0257212506 1.176277e-02
## 28 map04933 3 0.0031970353 5.458353e-04
## 29 map04660 4 0.0005321646 1.274726e-05
## 30 map04140 3 0.0304370792 1.429058e-02
## 31 map04013 3 0.0063424753 1.314903e-03
## 32 map04966 3 0.0015347815 1.497348e-04
## 33 map04659 3 0.0006034086 2.575524e-05
## 34 map04730 2 0.0187689187 7.553345e-03
## 35 map05212 2 0.0233863456 1.026718e-02
## 36 map04014 3 0.0132749942 3.927579e-03
## 37 map04658 3 0.0005321646 1.297962e-05
## 38 map04145 4 0.0035416249 6.262629e-04
## 39 map03010 5 0.0190401111 7.778582e-03
## 40 map05170 5 0.0011181095 6.135967e-05
## 41 map04724 2 0.0187689187 7.553345e-03
## 42 map01522 3 0.0015347815 1.497348e-04
## 43 map04915 2 0.0233863456 1.026718e-02
## 44 map04720 3 0.0021103215 2.702241e-04
## 45 map04071 3 0.0158654722 5.207747e-03
## 46 map04662 3 0.0015347815 1.497348e-04
## 47 map05211 2 0.0233863456 1.026718e-02
## 48 map05110 4 0.0011181095 5.873182e-05
## 49 map04625 4 0.0005321646 6.408062e-06
## 50 map04914 3 0.0095077430 2.550858e-03
## 51 map04725 2 0.0187689187 7.553345e-03
## 52 map04912 3 0.0021984656 3.485372e-04
## 53 map04010 4 0.0021984656 3.485146e-04
## 54 map04218 4 0.0021984656 3.485146e-04
## 55 map04062 2 0.0487989801 2.677993e-02
## 56 map05167 4 0.0014305661 8.722964e-05
## 57 map05132 2 0.0359258298 1.862009e-02
## 58 map04370 4 0.0005654846 1.724038e-05
## 59 map04371 2 0.0415437552 2.254509e-02
## 60 map05152 4 0.0016889605 2.008685e-04
## 61 map05219 2 0.0059792644 1.203145e-03
## 62 map04360 3 0.0057731981 1.126478e-03
## 63 map04072 3 0.0042482803 8.030286e-04
## 64 map04380 3 0.0015347815 1.497348e-04
## 65 map04620 2 0.0132749942 4.209145e-03
## 66 map04320 2 0.0094993686 2.490688e-03
## 67 map04150 6 0.0005321646 9.480172e-06
## 68 map04214 2 0.0311820012 1.502060e-02
## 69 map05161 3 0.0031970353 5.458353e-04
## 70 map05216 2 0.0132749942 4.209145e-03
## 71 map04540 2 0.0187689187 7.553345e-03
## 72 map04550 3 0.0015347815 1.497348e-04
## 73 map04664 3 0.0016889605 2.042701e-04
## 74 map04015 3 0.0075349143 1.748613e-03
## 75 map04722 3 0.0071319430 1.522061e-03
## 76 map04650 3 0.0016889605 2.042701e-04
## 77 map05218 2 0.0094993686 2.490688e-03
## 78 map04916 2 0.0179254596 6.339492e-03
## 79 map04917 3 0.0015347815 1.056434e-04
## 80 map04926 3 0.0042482803 8.030286e-04
## 81 map04210 2 0.0339716106 1.677866e-02
## 82 map05205 3 0.0115053167 3.193602e-03
## 83 map04022 2 0.0359258298 1.862009e-02
## 84 map05210 2 0.0359258298 1.862009e-02
## 85 map04726 2 0.0339716106 1.677866e-02
## 86 map05213 2 0.0187689187 7.553345e-03
## 87 map05214 2 0.0187689187 7.553345e-03
## 88 map05165 5 0.0016889605 2.059708e-04
## 89 map05215 2 0.0233863456 1.026718e-02
## 90 map05220 2 0.0132749942 4.209145e-03
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04972 map04972 4104 10 49 map04972
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04961 map04961 4104 9 49 map04961
## 3 https://www.kegg.jp/dbget-bin/www_bget?map04144 map04144 4104 74 49 map04144
## 4 https://www.kegg.jp/dbget-bin/www_bget?map05164 map05164 4104 27 49 map05164
## 5 https://www.kegg.jp/dbget-bin/www_bget?map04670 map04670 4104 14 49 map04670
## 6 https://www.kegg.jp/dbget-bin/www_bget?map05142 map05142 4104 9 49 map05142
## 7 https://www.kegg.jp/dbget-bin/www_bget?map04620 map04620 4104 9 49 map04620
## 8 https://www.kegg.jp/dbget-bin/www_bget?map04270 map04270 4104 11 49 map04270
## 9 https://www.kegg.jp/dbget-bin/www_bget?map04071 map04071 4104 32 49 map04071
## 10 https://www.kegg.jp/dbget-bin/www_bget?map05203 map05203 4104 43 49 map05203
## 11 https://www.kegg.jp/dbget-bin/www_bget?map04660 map04660 4104 14 49 map04660
## 12 https://www.kegg.jp/dbget-bin/www_bget?map04350 map04350 4104 9 49 map04350
## 13 https://www.kegg.jp/dbget-bin/www_bget?map05161 map05161 4104 15 49 map05161
## 14 https://www.kegg.jp/dbget-bin/www_bget?map04011 map04011 4104 69 49 map04011
## 15 https://www.kegg.jp/dbget-bin/www_bget?map04261 map04261 4104 15 49 map04261
## 16 https://www.kegg.jp/dbget-bin/www_bget?map05132 map05132 4104 19 49 map05132
## 17 https://www.kegg.jp/dbget-bin/www_bget?map04668 map04668 4104 11 49 map04668
## 18 https://www.kegg.jp/dbget-bin/www_bget?map05152 map05152 4104 27 49 map05152
## 19 https://www.kegg.jp/dbget-bin/www_bget?map00190 map00190 4104 77 49 map00190
## 20 https://www.kegg.jp/dbget-bin/www_bget?map04722 map04722 4104 21 49 map04722
## 21 https://www.kegg.jp/dbget-bin/www_bget?map04962 map04962 4104 14 49 map04962
## 22 https://www.kegg.jp/dbget-bin/www_bget?map04015 map04015 4104 22 49 map04015
## 23 https://www.kegg.jp/dbget-bin/www_bget?map05140 map05140 4104 6 49 map05140
## 24 https://www.kegg.jp/dbget-bin/www_bget?map03050 map03050 4104 37 49 map03050
## 25 https://www.kegg.jp/dbget-bin/www_bget?map04912 map04912 4104 13 49 map04912
## 26 https://www.kegg.jp/dbget-bin/www_bget?map05163 map05163 4104 30 49 map05163
## 27 https://www.kegg.jp/dbget-bin/www_bget?map04370 map04370 4104 15 49 map04370
## 28 https://www.kegg.jp/dbget-bin/www_bget?map04658 map04658 4104 5 49 map04658
## 29 https://www.kegg.jp/dbget-bin/www_bget?map04520 map04520 4104 12 49 map04520
## 30 https://www.kegg.jp/dbget-bin/www_bget?map04550 map04550 4104 10 49 map04550
## 31 https://www.kegg.jp/dbget-bin/www_bget?map05133 map05133 4104 8 49 map05133
## 32 https://www.kegg.jp/dbget-bin/www_bget?map04611 map04611 4104 20 49 map04611
## 33 https://www.kegg.jp/dbget-bin/www_bget?map04621 map04621 4104 21 49 map04621
## 34 https://www.kegg.jp/dbget-bin/www_bget?map04625 map04625 4104 12 49 map04625
## 35 https://www.kegg.jp/dbget-bin/www_bget?map04657 map04657 4104 11 49 map04657
## 36 https://www.kegg.jp/dbget-bin/www_bget?map04659 map04659 4104 6 49 map04659
## 37 https://www.kegg.jp/dbget-bin/www_bget?map04664 map04664 4104 11 49 map04664
## 38 https://www.kegg.jp/dbget-bin/www_bget?map04380 map04380 4104 10 49 map04380
## 39 https://www.kegg.jp/dbget-bin/www_bget?map04723 map04723 4104 37 49 map04723
## 40 https://www.kegg.jp/dbget-bin/www_bget?map01522 map01522 4104 10 49 map01522
## 41 https://www.kegg.jp/dbget-bin/www_bget?map05131 map05131 4104 21 49 map05131
## 42 https://www.kegg.jp/dbget-bin/www_bget?map05205 map05205 4104 27 49 map05205
## 43 https://www.kegg.jp/dbget-bin/www_bget?map04928 map04928 4104 10 49 map04928
## 44 https://www.kegg.jp/dbget-bin/www_bget?map04917 map04917 4104 9 49 map04917
## 45 https://www.kegg.jp/dbget-bin/www_bget?map04933 map04933 4104 15 49 map04933
## 46 https://www.kegg.jp/dbget-bin/www_bget?map04810 map04810 4104 30 49 map04810
## 47 https://www.kegg.jp/dbget-bin/www_bget?map05145 map05145 4104 12 49 map05145
## nt padj pval
## 1 2 0.034095598 5.912532e-03
## 2 2 0.034095598 4.766232e-03
## 3 5 0.022709413 1.709701e-03
## 4 3 0.034095598 3.825512e-03
## 5 2 0.047772614 1.159798e-02
## 6 2 0.034095598 4.766232e-03
## 7 2 0.034095598 4.766232e-03
## 8 2 0.035448075 7.171576e-03
## 9 3 0.034719370 6.221390e-03
## 10 5 0.007776158 1.348467e-04
## 11 3 0.013121917 5.309446e-04
## 12 2 0.034095598 4.766232e-03
## 13 2 0.048885494 1.328103e-02
## 14 4 0.039964206 8.778265e-03
## 15 2 0.048885494 1.328103e-02
## 16 3 0.022709413 1.355245e-03
## 17 2 0.035448075 7.171576e-03
## 18 4 0.011128510 2.573066e-04
## 19 4 0.048885494 1.281780e-02
## 20 4 0.007776158 9.249959e-05
## 21 3 0.013121917 5.309446e-04
## 22 3 0.022709413 2.100293e-03
## 23 2 0.022709413 2.031959e-03
## 24 3 0.040429016 9.347749e-03
## 25 2 0.042266732 1.001697e-02
## 26 3 0.034095598 5.178338e-03
## 27 2 0.048885494 1.328103e-02
## 28 2 0.022709413 1.365042e-03
## 29 2 0.039933175 8.540621e-03
## 30 2 0.034095598 5.912532e-03
## 31 3 0.007776158 8.591865e-05
## 32 3 0.022709413 1.581075e-03
## 33 3 0.022709413 1.829171e-03
## 34 3 0.011291670 3.263489e-04
## 35 2 0.035448075 7.171576e-03
## 36 2 0.022709413 2.031959e-03
## 37 2 0.035448075 7.171576e-03
## 38 2 0.034095598 5.912532e-03
## 39 3 0.040429016 9.347749e-03
## 40 2 0.034095598 5.912532e-03
## 41 3 0.022709413 1.829171e-03
## 42 3 0.034095598 3.825512e-03
## 43 2 0.034095598 5.912532e-03
## 44 2 0.034095598 4.766232e-03
## 45 2 0.048885494 1.328103e-02
## 46 3 0.034095598 5.178338e-03
## 47 2 0.039933175 8.540621e-03
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 526
## name nt padj pval
## 1 map03010 34 0.0001806124 5.921717e-07
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04120 map04120 4104 57 523 map04120
## nt padj pval
## 1 23 3.470379e-05 1.309577e-07
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 72 map03010
## nt padj pval
## 1 18 3.748328e-11 2.166664e-13
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map01130 map01130 4104 220 296
## 2 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 296
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00290 map00290 4104 10 296
## 4 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 296
## 5 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 296
## name nt padj pval
## 1 map01130 34 1.058386e-03 1.207284e-05
## 2 map01100 95 2.145563e-03 3.263213e-05
## 3 map00290 5 1.849854e-02 3.516833e-04
## 4 map03010 28 6.268560e-07 2.383483e-09
## 5 map01110 48 7.204311e-06 5.478564e-08
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03013 map03013 4104 97 379 map03013
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04120 map04120 4104 57 379 map04120
## nt padj pval
## 1 23 0.001916483 1.503124e-05
## 2 17 0.001916483 7.922014e-06
##
## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 784
## 2 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 784
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00040 map00040 4104 20 784
## name nt padj pval
## 1 map01100 213 3.138580e-02 1.868202e-04
## 2 map03010 62 1.498964e-15 4.461201e-18
## 3 map00040 11 4.010626e-02 3.580916e-04
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04111 map04111 4104 97 779 map04111
## 2 https://www.kegg.jp/dbget-bin/www_bget?map03015 map03015 4104 46 779 map03015
## 3 https://www.kegg.jp/dbget-bin/www_bget?map03013 map03013 4104 97 779 map03013
## 4 https://www.kegg.jp/dbget-bin/www_bget?map04120 map04120 4104 57 779 map04120
## 5 https://www.kegg.jp/dbget-bin/www_bget?map00970 map00970 4104 26 779 map00970
## nt padj pval
## 1 33 0.01914279 2.774317e-04
## 2 19 0.02011855 3.644664e-04
## 3 34 0.01261060 1.158509e-04
## 4 23 0.01261060 1.370717e-04
## 5 15 0.00346308 1.254739e-05
##
## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 525
## 2 https://www.kegg.jp/dbget-bin/www_bget?map01120 map01120 4104 184 525
## 3 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 525
## name nt padj pval
## 1 map01100 154 0.009458785 3.121711e-05
## 2 map01120 41 0.018324674 1.814324e-04
## 3 map01110 61 0.014912736 9.843390e-05
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03015 map03015 4104 46 506 map03015
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04120 map04120 4104 57 506 map04120
## 3 https://www.kegg.jp/dbget-bin/www_bget?map03050 map03050 4104 37 506 map03050
## 4 https://www.kegg.jp/dbget-bin/www_bget?map03022 map03022 4104 31 506 map03022
## nt padj pval
## 1 17 0.0019147536 1.513639e-05
## 2 18 0.0081671145 9.684325e-05
## 3 16 0.0006136239 2.425391e-06
## 4 11 0.0472663021 7.472933e-04
##
## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 658
## name nt padj pval
## 1 map03010 41 2.114278e-05 6.485516e-08
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03015 map03015 4104 46 624 map03015
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04120 map04120 4104 57 624 map04120
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00970 map00970 4104 26 624 map00970
## nt padj pval
## 1 17 0.02096287 0.0002303612
## 2 20 0.02096287 0.0001512537
## 3 12 0.02096287 0.0001703051
##
## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00400 map00400 4104 23 492
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04714 map04714 4104 96 492
## 3 https://www.kegg.jp/dbget-bin/www_bget?map05012 map05012 4104 64 492
## 4 https://www.kegg.jp/dbget-bin/www_bget?map01130 map01130 4104 220 492
## 5 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 492
## 6 https://www.kegg.jp/dbget-bin/www_bget?map04723 map04723 4104 37 492
## 7 https://www.kegg.jp/dbget-bin/www_bget?map00220 map00220 4104 19 492
## 8 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 492
## 9 https://www.kegg.jp/dbget-bin/www_bget?map00250 map00250 4104 30 492
## 10 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 492
## 11 https://www.kegg.jp/dbget-bin/www_bget?map00500 map00500 4104 32 492
## 12 https://www.kegg.jp/dbget-bin/www_bget?map05152 map05152 4104 27 492
## 13 https://www.kegg.jp/dbget-bin/www_bget?map01120 map01120 4104 184 492
## 14 https://www.kegg.jp/dbget-bin/www_bget?map00020 map00020 4104 21 492
## 15 https://www.kegg.jp/dbget-bin/www_bget?map00190 map00190 4104 77 492
## 16 https://www.kegg.jp/dbget-bin/www_bget?map01230 map01230 4104 103 492
## 17 https://www.kegg.jp/dbget-bin/www_bget?map05010 map05010 4104 62 492
## 18 https://www.kegg.jp/dbget-bin/www_bget?map00052 map00052 4104 17 492
## 19 https://www.kegg.jp/dbget-bin/www_bget?map05322 map05322 4104 8 492
## 20 https://www.kegg.jp/dbget-bin/www_bget?map01210 map01210 4104 27 492
## 21 https://www.kegg.jp/dbget-bin/www_bget?map01200 map01200 4104 87 492
## 22 https://www.kegg.jp/dbget-bin/www_bget?map05016 map05016 4104 76 492
## 23 https://www.kegg.jp/dbget-bin/www_bget?map00010 map00010 4104 32 492
## 24 https://www.kegg.jp/dbget-bin/www_bget?map00710 map00710 4104 17 492
## name nt padj pval
## 1 map00400 8 4.723088e-02 3.829531e-03
## 2 map04714 25 2.530164e-03 1.025742e-04
## 3 map05012 18 7.208510e-03 3.452491e-04
## 4 map01130 51 6.292990e-05 1.275606e-06
## 5 map03010 51 7.056602e-17 2.383987e-19
## 6 map04723 11 3.913672e-02 3.026433e-03
## 7 map00220 8 1.500530e-02 9.124845e-04
## 8 map01100 164 1.603042e-07 1.083136e-09
## 9 map00250 11 7.828269e-03 4.231497e-04
## 10 map01110 65 3.758746e-05 6.349233e-07
## 11 map00500 14 2.359773e-04 6.377765e-06
## 12 map05152 10 1.229563e-02 7.061678e-04
## 13 map01120 47 1.640730e-05 1.662902e-07
## 14 map00020 8 2.923328e-02 1.975222e-03
## 15 map00190 24 2.244725e-04 5.308471e-06
## 16 map01230 31 3.758746e-05 5.265859e-07
## 17 map05010 20 6.080503e-04 1.848801e-05
## 18 map00052 7 3.175815e-02 2.253112e-03
## 19 map05322 5 1.553480e-02 9.971665e-04
## 20 map01210 9 3.913672e-02 3.041029e-03
## 21 map01200 24 1.395969e-03 5.187722e-05
## 22 map05016 21 3.380494e-03 1.484677e-04
## 23 map00010 13 1.069408e-03 3.612864e-05
## 24 map00710 8 7.208510e-03 3.652961e-04
##
## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03013 map03013 4104 97 549
## 2 https://www.kegg.jp/dbget-bin/www_bget?map03015 map03015 4104 46 549
## 3 None map00000 4104 1631 549
## name nt padj pval
## 1 map03013 28 0.008743032 3.885792e-05
## 2 map03015 15 0.045736360 6.098181e-04
## 3 None 256 0.028682961 2.549597e-04
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03050 map03050 4104 37 569
## 2 https://www.kegg.jp/dbget-bin/www_bget?map03013 map03013 4104 97 569
## 3 https://www.kegg.jp/dbget-bin/www_bget?map00480 map00480 4104 23 569
## 4 https://www.kegg.jp/dbget-bin/www_bget?map04120 map04120 4104 57 569
## 5 https://www.kegg.jp/dbget-bin/www_bget?map04530 map04530 4104 27 569
## 6 https://www.kegg.jp/dbget-bin/www_bget?map03015 map03015 4104 46 569
## 7 https://www.kegg.jp/dbget-bin/www_bget?map01230 map01230 4104 103 569
## 8 https://www.kegg.jp/dbget-bin/www_bget?map00970 map00970 4104 26 569
## name nt padj pval
## 1 map03050 17 0.0003106069 2.195102e-06
## 2 map03013 26 0.0204738875 4.943129e-04
## 3 map00480 10 0.0204738875 5.064212e-04
## 4 map04120 20 0.0028160353 3.980262e-05
## 5 map04530 12 0.0060534321 1.069511e-04
## 6 map03015 19 0.0003756707 3.982374e-06
## 7 map01230 26 0.0465450226 1.315760e-03
## 8 map00970 14 0.0003106069 1.611887e-06
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04915 map04915 4104 14 71 map04915
## 2 https://www.kegg.jp/dbget-bin/www_bget?map04150 map04150 4104 46 71 map04150
## 3 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 71 map03010
## 4 https://www.kegg.jp/dbget-bin/www_bget?map03050 map03050 4104 37 71 map03050
## 5 https://www.kegg.jp/dbget-bin/www_bget?map05203 map05203 4104 43 71 map05203
## 6 https://www.kegg.jp/dbget-bin/www_bget?map05152 map05152 4104 27 71 map05152
## nt padj pval
## 1 3 0.0462145149 1.575495e-03
## 2 6 0.0103361555 1.174563e-04
## 3 11 0.0004349367 2.471231e-06
## 4 5 0.0223572729 3.810899e-04
## 5 5 0.0341656988 7.764932e-04
## 6 4 0.0376204057 1.068762e-03
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00620 map00620 4104 33 211
## 2 https://www.kegg.jp/dbget-bin/www_bget?map01100 map01100 4104 914 211
## 3 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 211
## 4 https://www.kegg.jp/dbget-bin/www_bget?map00660 map00660 4104 5 211
## 5 https://www.kegg.jp/dbget-bin/www_bget?map00290 map00290 4104 10 211
## 6 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 211
## 7 https://www.kegg.jp/dbget-bin/www_bget?map00600 map00600 4104 21 211
## 8 https://www.kegg.jp/dbget-bin/www_bget?map01210 map01210 4104 27 211
## 9 https://www.kegg.jp/dbget-bin/www_bget?map03050 map03050 4104 37 211
## 10 https://www.kegg.jp/dbget-bin/www_bget?map00040 map00040 4104 20 211
## 11 https://www.kegg.jp/dbget-bin/www_bget?map00250 map00250 4104 30 211
## name nt padj pval
## 1 map00620 7 2.728099e-02 1.167669e-03
## 2 map01100 77 1.270843e-04 9.889827e-07
## 3 map03010 32 4.327094e-14 1.683694e-16
## 4 map00660 4 2.089899e-03 3.262735e-05
## 5 map00290 5 2.993541e-03 6.988812e-05
## 6 map01110 31 4.137463e-03 1.126936e-04
## 7 map00600 6 1.390454e-02 4.869292e-04
## 8 map01210 8 2.089899e-03 4.065952e-05
## 9 map03050 10 9.167252e-04 1.070107e-05
## 10 map00040 6 1.166813e-02 3.632104e-04
## 11 map00250 7 1.631382e-02 6.347790e-04
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03022 map03022 4104 31 175 map03022
## nt padj pval
## 1 7 0.03258832 0.0002506794
##
## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map03010 map03010 4104 112 403
## name nt padj pval
## 1 map03010 32 2.905131e-06 1.096276e-08
##
## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## list()## No enrichments found in task: ko_pathway## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map00900 map00900 4104 20 6 map00900
## nt padj pval
## 1 2 0.004683883 0.0003345631
##
## $ko_pathway
## def id m mt n
## 1 https://www.kegg.jp/dbget-bin/www_bget?map05012 map05012 4104 64 219
## 2 https://www.kegg.jp/dbget-bin/www_bget?map01110 map01110 4104 301 219
## 3 https://www.kegg.jp/dbget-bin/www_bget?map04145 map04145 4104 36 219
## 4 https://www.kegg.jp/dbget-bin/www_bget?map05016 map05016 4104 76 219
## 5 https://www.kegg.jp/dbget-bin/www_bget?map05152 map05152 4104 27 219
## 6 https://www.kegg.jp/dbget-bin/www_bget?map00190 map00190 4104 77 219
## 7 https://www.kegg.jp/dbget-bin/www_bget?map05010 map05010 4104 62 219
## name nt padj pval
## 1 map05012 13 0.002473681 2.311852e-05
## 2 map01110 29 0.033844851 1.107075e-03
## 3 map04145 8 0.020436994 4.774999e-04
## 4 map05016 12 0.020903724 5.860857e-04
## 5 map05152 8 0.003793601 5.318133e-05
## 6 map00190 13 0.009309519 1.740097e-04
## 7 map05010 13 0.002473681 1.608515e-05
##
## $ko_pathway
## def id m mt n name
## 1 https://www.kegg.jp/dbget-bin/www_bget?map04110 map04110 4104 53 263 map04110
## nt padj pval
## 1 12 0.01509714 9.319225e-055.4.1 Control
plotResults(control.res.enr)## <H3>20Cvs19C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes## Loading required package: treemap## Loading required package: RColorBrewer## Loading required package: KEGGREST
##
## <hr><H3>21Cvs20C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>22Cvs21C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>23Cvs22C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>24Cvs23C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>25Cvs24C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr><H3>26Cvs25C</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>28Cvs26C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>31Cvs28C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>32Cvs31C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr><H3>34Cvs32C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr><H3>35Cvs34C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>36Cvs35C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>37Cvs36C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>38Cvs37C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>39Cvs38C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>40Cvs39C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>41Cvs40C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr>5.4.2 Fertilised
plotResults(fertilised.res.enr)## <H3>20Fvs19F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>21Fvs20F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>22Fvs21F</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>23Fvs22F</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>24Fvs23F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>25Fvs24F</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>26Fvs25F</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>28Fvs26F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr><H3>31Fvs28F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>32Fvs31F</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>34Fvs32F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr><H3>35Fvs34F</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>36Fvs35F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr><H3>37Fvs36F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>38Fvs37F</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>39Fvs38F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>40Fvs39F</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr><H3>41Fvs40F</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr>5.4.3 Combined
plotResults(combined.res.enr)## <H3>19Fvs19C</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>20Fvs20C</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>21Fvs21C</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>22Fvs22C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>23Fvs23C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>24Fvs24C</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>25Fvs25C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>26Fvs26C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>28Fvs28C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>31Fvs31C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>32Fvs32C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>34Fvs34C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>35Fvs35C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr><H3>36Fvs36C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>37Fvs37C</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>38Fvs38C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr><H3>39Fvs39C</H3>
##
## Up genes
##
## <hr>Down genes
##
## No enrichment data found
## <hr><H3>40Fvs40C</H3>
##
## Up genes
##
## No enrichment data found
## <hr>Down genes
##
## <hr><H3>41Fvs41C</H3>
##
## Up genes
##
## <hr>Down genes
##
## <hr>6 Session information
sessionInfo()## R version 3.6.2 (2019-12-12)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] KEGGREST_1.26.1 RColorBrewer_1.1-2
## [3] treemap_2.4-2 jsonlite_1.6.1
## [5] tibble_2.1.3 tidyr_1.0.2
## [7] here_0.1 dplyr_0.8.4
## [9] plotly_4.9.2 ggplot2_3.3.0
## [11] tximport_1.14.0 DESeq2_1.26.0
## [13] SummarizedExperiment_1.16.1 DelayedArray_0.12.2
## [15] BiocParallel_1.20.1 matrixStats_0.56.0
## [17] Biobase_2.46.0 GenomicRanges_1.38.0
## [19] GenomeInfoDb_1.22.0 IRanges_2.20.2
## [21] S4Vectors_0.24.3 BiocGenerics_0.32.0
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 bit64_0.9-7 httr_1.4.1
## [4] rprojroot_1.3-2 tools_3.6.2 backports_1.1.5
## [7] R6_2.4.1 rpart_4.1-15 Hmisc_4.3-1
## [10] DBI_1.1.0 lazyeval_0.2.2 colorspace_1.4-1
## [13] nnet_7.3-13 withr_2.1.2 tidyselect_1.0.0
## [16] gridExtra_2.3 curl_4.3 bit_1.1-15.2
## [19] compiler_3.6.2 htmlTable_1.13.3 labeling_0.3
## [22] scales_1.1.0 checkmate_2.0.0 genefilter_1.68.0
## [25] stringr_1.4.0 digest_0.6.25 foreign_0.8-76
## [28] rmarkdown_2.1 XVector_0.26.0 base64enc_0.1-3
## [31] jpeg_0.1-8.1 pkgconfig_2.0.3 htmltools_0.4.0
## [34] fastmap_1.0.1 htmlwidgets_1.5.1 rlang_0.4.5
## [37] rstudioapi_0.11 RSQLite_2.2.0 shiny_1.4.0.2
## [40] farver_2.0.3 crosstalk_1.1.0.1 acepack_1.4.1
## [43] RCurl_1.98-1.1 magrittr_1.5 GenomeInfoDbData_1.2.2
## [46] Formula_1.2-3 Matrix_1.2-18 Rcpp_1.0.4
## [49] munsell_0.5.0 lifecycle_0.2.0 stringi_1.4.6
## [52] yaml_2.2.1 zlibbioc_1.32.0 grid_3.6.2
## [55] blob_1.2.1 promises_1.1.0 crayon_1.3.4
## [58] lattice_0.20-40 Biostrings_2.54.0 splines_3.6.2
## [61] annotate_1.64.0 locfit_1.5-9.4 knitr_1.28
## [64] pillar_1.4.3 igraph_1.2.5 geneplotter_1.64.0
## [67] XML_3.99-0.3 glue_1.3.2 evaluate_0.14
## [70] latticeExtra_0.6-29 data.table_1.12.8 httpuv_1.5.2
## [73] png_0.1-7 vctrs_0.2.4 gtable_0.3.0
## [76] purrr_0.3.3 assertthat_0.2.1 gridBase_0.4-7
## [79] xfun_0.12 mime_0.9 xtable_1.8-4
## [82] later_1.0.0 survival_3.1-11 viridisLite_0.3.0
## [85] AnnotationDbi_1.48.0 memoise_1.1.0 cluster_2.1.0